Difference between revisions of "2022 Denovo tutorial 2 with PDBID 4ZUD"

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  grep -wc MOLECULE *.mol2
 
  grep -wc MOLECULE *.mol2
  
−
[[File:4ZUD_minimized_lig_outline_&_scaffold(1).png|thumb|center|500px|'''The figures show the fragments generated from the ligand in the 4ZUD crystal structure. Center plot are scaffolds, left are side chains, and right are linkers. The reference ligand is translucent in all figures.''']]
+
 
−
[[File:4ZUD_minimized_lig_outline_&_linkers.png|thumb|right|300px]]
+
[[File:4ZUD_minimized_lig_outline_&_linkers.png|thumb|center|300px|'''Fragment Linker(s)''']]
−
[[File:4ZUD_minimized_lig_outline_&_sidechains.png|thumb|left|300px]]  
+
[[File:4ZUD_minimized_lig_outline_&_scaffold(1).png|thumb|center|300px|'''Fragment Scaffold(s)''']]  
 +
[[File:4ZUD_minimized_lig_outline_&_sidechains.png|thumb|center|300px|'''Fragment Side Chain(s)''']]
  
 
==='''Focused De Novo Growth'''===
 
==='''Focused De Novo Growth'''===
  
−
Now we can use the fragments generated in the previous step to allow DOCK to make new molecules that fall within certain rotamers, molecular weights, charges and chemical group compositions. DOCK will generate all possible molecules within the given parameters and that fall within resonable internal energies based on the AMBER van der Waals equation.  
+
Now we can use the fragments generated in the previous step to allow DOCK to make new molecules that fall within certain rotamers, molecular weights, charges and chemical group compositions. DOCK will generate all possible molecules within the given parameters and that fall within reasonable internal energies based on the AMBER van der Waals equation.  
  
 
In a new directory:
 
In a new directory:
Line 139: Line 140:
 
Although we've generated a variety of new molecules, all composed of the 4ZUD native ligand fragments, they were created under the energetic constraints of an ''in silico'' environment, thus although these new molecules bare similarity to the crystal ligand, many will not be yield viable interaction energies with the 4ZUD receptor.  
 
Although we've generated a variety of new molecules, all composed of the 4ZUD native ligand fragments, they were created under the energetic constraints of an ''in silico'' environment, thus although these new molecules bare similarity to the crystal ligand, many will not be yield viable interaction energies with the 4ZUD receptor.  
  
−
In order to shorten the list of potential molecules, and to ensure we only focus on ones that form similar interaction with the protein active site relative to the crystal ligand, we can apply a
+
In order to shorten the list of potential molecules, and to ensure we only focus on ones that form similar interactions with the protein active site relative to the crystal ligand, we can apply a rescoring function to the new molecule library to extract those that are similar to the crystal ligand in both general composition, and energetic interactions with the protein.
 +
 
 +
In an new directory:
 +
 
 +
mkdir dn_focused_rescore
 +
 
 +
In a new input file:
 +
 
 +
vim rescore.in
 +
 
 +
Insert the following:
 +
 
 +
conformer_search_type                                        rigid
 +
use_internal_energy                                          yes
 +
internal_energy_rep_exp                                      12
 +
internal_energy_cutoff                                      100.0
 +
ligand_atom_file                                            ../dn_focused_growth/dn_focus.out.denovo_build.mol2
 +
limit_max_ligands                                            no
 +
skip_molecule                                                no
 +
read_mol_solvation                                          no
 +
calculate_rmsd                                              no
 +
use_database_filter                                          no
 +
orient_ligand                                                no
 +
bump_filter                                                  no
 +
score_molecules                                              yes
 +
contact_score_primary                                        no
 +
contact_score_secondary                                      no
 +
grid_score_primary                                          no
 +
grid_score_secondary                                        no
 +
multigrid_score_primary                                      no
 +
multigrid_score_secondary                                    no
 +
dock3.5_score_primary                                        no
 +
dock3.5_score_secondary                                      no
 +
continuous_score_primary                                    no
 +
continuous_score_secondary                                  no
 +
footprint_similarity_score_primary                          no
 +
footprint_similarity_score_secondary                        no
 +
pharmacophore_score_primary                                  no
 +
pharmacophore_score_secondary                                no
 +
descriptor_score_primary                                    yes
 +
descriptor_score_secondary                                  no
 +
descriptor_use_grid_score                                    no
 +
descriptor_use_multigrid_score                              no
 +
descriptor_use_continuous_score                              no
 +
descriptor_use_footprint_similarity                          yes
 +
descriptor_use_pharmacophore_score                          yes
 +
descriptor_use_tanimoto                                      yes
 +
descriptor_use_hungarian                                    yes
 +
descriptor_use_volume_overlap                                yes
 +
descriptor_fps_score_use_footprint_reference_mol2            yes
 +
descriptor_fps_score_footprint_reference_mol2_filename      ../../003.gridbox/4zud.lig.min_scored.mol2
 +
descriptor_fps_score_foot_compare_type                      Euclidean
 +
descriptor_fps_score_normalize_foot                          no
 +
descriptor_fps_score_foot_comp_all_residue                  yes
 +
descriptor_fps_score_receptor_filename                      ../../001.structure/4ZUD_protein_hydrogens.mol2
 +
descriptor_fps_score_vdw_att_exp                            6
 +
descriptor_fps_score_vdw_rep_exp                            12
 +
descriptor_fps_score_vdw_rep_rad_scale                      1
 +
descriptor_fps_score_use_distance_dependent_dielectric      yes
 +
descriptor_fps_score_dielectric                              4.0
 +
descriptor_fps_score_vdw_fp_scale                            1
 +
descriptor_fps_score_es_fp_scale                            1
 +
descriptor_fps_score_hb_fp_scale                            0
 +
descriptor_fms_score_use_ref_mol2                            yes
 +
descriptor_fms_score_ref_mol2_filename                      ../../003.gridbox/4zud.lig.min_scored.mol2
 +
descriptor_fms_score_write_reference_pharmacophore_mol2      no
 +
descriptor_fms_score_write_reference_pharmacophore_txt      no
 +
descriptor_fms_score_write_candidate_pharmacophore          no
 +
descriptor_fms_score_write_matched_pharmacophore            no
 +
descriptor_fms_score_compare_type                            overlap
 +
descriptor_fms_score_full_match                              yes
 +
descriptor_fms_score_match_rate_weight                      5.0
 +
descriptor_fms_score_match_dist_cutoff                      1.0
 +
descriptor_fms_score_match_proj_cutoff                      0.7071
 +
descriptor_fms_score_max_score                              20
 +
descriptor_fingerprint_ref_filename                          ../../003.gridbox/4zud.lig.min_scored.mol2
 +
descriptor_hms_score_ref_filename                            ../../003.gridbox/4zud.lig.min_scored.mol2
 +
descriptor_hms_score_matching_coeff                          -5
 +
descriptor_hms_score_rmsd_coeff                              1
 +
descriptor_volume_score_reference_mol2_filename              ../../003.gridbox/4zud.lig.min_scored.mol2
 +
descriptor_volume_score_overlap_compute_method              analytical
 +
descriptor_weight_fps_score                                  1
 +
descriptor_weight_pharmacophore_score                        1
 +
descriptor_weight_fingerprint_tanimoto                      -1
 +
descriptor_weight_hms_score                                  1
 +
descriptor_weight_volume_overlap_score                      -1
 +
gbsa_zou_score_secondary                                    no
 +
gbsa_hawkins_score_secondary                                no
 +
SASA_score_secondary                                        no
 +
amber_score_secondary                                        no
 +
minimize_ligand                                              no
 +
atom_model                                                  all
 +
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
 +
flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
 +
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
 +
chem_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/chem.defn
 +
pharmacophore_defn_file                                      /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/ph4.defn
 +
ligand_outfile_prefix                                        descriptor.output
 +
write_footprints                                            yes
 +
write_hbonds                                                yes
 +
write_orientations                                          no
 +
num_scored_conformers                                        1
 +
rank_ligands                                                no
 +
 
 +
Run the command using:
 +
 
 +
dock6 -i rescore.in -o rescore.out
 +
 
 +
Several files should have been created. The '''descriptor.output_scored.mol2''' file contains all of the molecules that would be deemed 'viable' in terms of mimicking the native crystal ligand interactions with the protein active site residues.
 +
 
 +
Footprint analysis plots can be generated for each molecule individually. Follow the steps provided in the previous tutorial: [[2022 DOCK tutorial 2 with PDBID 4ZUD]]
 +
 
 +
Native crystal molecule for reference:
 +
[[File:4ZUD_minimized_lig(1).png|thumb|center|500px|]]
 +
 
 +
The molecule with the smallest footprint score: '''7.127408'''
 +
[[File:4ZUD lowestFPscore denovo molecule new(1).png|thumb|center|500px|]]
 +
[[File:Compoud221 footprint.txt.png|thumb|center|500px|]]
 +
 
 +
The molecule with the largest footprint score: '''26.976864'''
 +
[[File:4ZUD highestFPscore denovo molecule.png|thumb|center|500px|]]
 +
[[File:Compoud193 footprint.txt.png|thumb|center|500px|]]

Latest revision as of 15:56, 7 March 2022

De Novo Design

De novo design refers to the process of generating novel ligands in an effort to identify molecules of physiological significance that can be further optimized to become approved drug molecules. The synthesis of thousands of potential drug molecules are done experimentally daily, but with computers, millions of molecules can be computationally modelled and pre-selected for possible synthesis in a fraction of the time it would take to test all possible molecules solely experimentally. With this, scientists are able to direct their attention towards molecules that have the highest probability of imparting a therapeutic effect upon binding to a respective receptor.

This tutorial is the second part of the 2022 DOCK tutorial 2 with PDBID 4ZUD tutorial. You will need the files created in that tutorial to continue with this one!

Make a new directory to organize the files generated in this tutorial: 

mkdir 005.denovo

Fragment Library Generation

To create new molecules, we need to begin with the building blocks. For the purposes of speed, we most often use pre-defined molecular fragments that can be arranged/attached in a variety of orientations to create unique structures. Since we have the structure of a ligand that is known to bind the 4ZUD protein, we can generate fragments from that molecule to increase the probability of creating molecules with similar properties to the known ligand.

In an input file: 

vim fragment.in

Insert the following: 

conformer_search_type                                        flex
write_fragment_libraries                                     yes
fragment_library_prefix                                      fraglib
fragment_library_freq_cutoff                                 1
fragment_library_sort_method                                 freq
fragment_library_trans_origin                                no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../001.structure/4ZUD_ligand_hydrogens.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../002.surface_spheres/selected_spheres.sph
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
bump_filter                                                  no
score_molecules                                              no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
ligand_outfile_prefix                                        fragment.out
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

Run the fragment generation with the following command: 

dock6 -i fragment.in -o fragment.out

DOCK should generate six files; three of those files should be mol2's of linker, scaffold, and side chain fragments. You can extract the number of fragments present in each file by running: 

grep -wc MOLECULE *.mol2


Fragment Linker(s)
Fragment Scaffold(s)
Fragment Side Chain(s)

Focused De Novo Growth

Now we can use the fragments generated in the previous step to allow DOCK to make new molecules that fall within certain rotamers, molecular weights, charges and chemical group compositions. DOCK will generate all possible molecules within the given parameters and that fall within reasonable internal energies based on the AMBER van der Waals equation.

In a new directory: 

mkdir dn_focused_growth

In an input file: 

vim dn_focus.in

Insert the following: 

conformer_search_type                                        denovo
dn_fraglib_scaffold_file                                     ../fraglib_scaffold.mol2
dn_fraglib_linker_file                                       ../fraglib_linker.mol2
dn_fraglib_sidechain_file                                    ../fraglib_sidechain.mol2
dn_user_specified_anchor                                     no
dn_use_torenv_table                                          yes
dn_torenv_table                                              ../fraglib_torenv.dat
dn_sampling_method                                           graph
dn_graph_max_picks                                           30
dn_graph_breadth                                             3
dn_graph_depth                                               2
dn_graph_temperature                                         100.0
dn_pruning_conformer_score_cutoff                            100.0
dn_pruning_conformer_score_scaling_factor                    1.0
dn_pruning_clustering_cutoff                                 100.0
dn_constraint_mol_wt                                         550.0
dn_constraint_rot_bon                                        15
dn_constraint_formal_charge                                  2.0
dn_heur_unmatched_num                                        1
dn_heur_matched_rmsd                                         2.0
dn_unique_anchors                                            1
dn_max_grow_layers                                           9
dn_max_root_size                                             25
dn_max_layer_size                                            25
dn_max_current_aps                                           5
dn_max_scaffolds_per_layer                                   1
dn_write_checkpoints                                         yes
dn_write_prune_dump                                          no
dn_write_orients                                             no
dn_write_growth_trees                                        no
dn_output_prefix                                             dn_focus.out
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../../002.surface_spheres/selected_spheres.sph
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           yes
grid_score_secondary                                         no

Run this calculation with the following command: 

dock6 -i dn_focus.in -o dn_focus.out

A few files will be generated, but the main file with all of the de novo molecules in a mol2 format is dn_focus.out.denovo_build.mol2. If you look at the dn_focus.out file you can see the number of molecules created which should be around 23,000.


Focused De Novo Rescored

Although we've generated a variety of new molecules, all composed of the 4ZUD native ligand fragments, they were created under the energetic constraints of an in silico environment, thus although these new molecules bare similarity to the crystal ligand, many will not be yield viable interaction energies with the 4ZUD receptor.

In order to shorten the list of potential molecules, and to ensure we only focus on ones that form similar interactions with the protein active site relative to the crystal ligand, we can apply a rescoring function to the new molecule library to extract those that are similar to the crystal ligand in both general composition, and energetic interactions with the protein.

In an new directory: 

mkdir dn_focused_rescore

In a new input file: 

vim rescore.in

Insert the following: 

conformer_search_type                                        rigid
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../dn_focused_growth/dn_focus.out.denovo_build.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          no
orient_ligand                                                no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
multigrid_score_primary                                      no
multigrid_score_secondary                                    no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     no
continuous_score_secondary                                   no
footprint_similarity_score_primary                           no
footprint_similarity_score_secondary                         no
pharmacophore_score_primary                                  no
pharmacophore_score_secondary                                no
descriptor_score_primary                                     yes
descriptor_score_secondary                                   no
descriptor_use_grid_score                                    no
descriptor_use_multigrid_score                               no
descriptor_use_continuous_score                              no
descriptor_use_footprint_similarity                          yes
descriptor_use_pharmacophore_score                           yes
descriptor_use_tanimoto                                      yes
descriptor_use_hungarian                                     yes
descriptor_use_volume_overlap                                yes
descriptor_fps_score_use_footprint_reference_mol2            yes
descriptor_fps_score_footprint_reference_mol2_filename       ../../003.gridbox/4zud.lig.min_scored.mol2
descriptor_fps_score_foot_compare_type                       Euclidean
descriptor_fps_score_normalize_foot                          no
descriptor_fps_score_foot_comp_all_residue                   yes
descriptor_fps_score_receptor_filename                       ../../001.structure/4ZUD_protein_hydrogens.mol2
descriptor_fps_score_vdw_att_exp                             6
descriptor_fps_score_vdw_rep_exp                             12
descriptor_fps_score_vdw_rep_rad_scale                       1
descriptor_fps_score_use_distance_dependent_dielectric       yes
descriptor_fps_score_dielectric                              4.0
descriptor_fps_score_vdw_fp_scale                            1
descriptor_fps_score_es_fp_scale                             1
descriptor_fps_score_hb_fp_scale                             0
descriptor_fms_score_use_ref_mol2                            yes
descriptor_fms_score_ref_mol2_filename                       ../../003.gridbox/4zud.lig.min_scored.mol2
descriptor_fms_score_write_reference_pharmacophore_mol2      no
descriptor_fms_score_write_reference_pharmacophore_txt       no
descriptor_fms_score_write_candidate_pharmacophore           no
descriptor_fms_score_write_matched_pharmacophore             no
descriptor_fms_score_compare_type                            overlap
descriptor_fms_score_full_match                              yes
descriptor_fms_score_match_rate_weight                       5.0
descriptor_fms_score_match_dist_cutoff                       1.0
descriptor_fms_score_match_proj_cutoff                       0.7071
descriptor_fms_score_max_score                               20
descriptor_fingerprint_ref_filename                          ../../003.gridbox/4zud.lig.min_scored.mol2
descriptor_hms_score_ref_filename                            ../../003.gridbox/4zud.lig.min_scored.mol2
descriptor_hms_score_matching_coeff                          -5
descriptor_hms_score_rmsd_coeff                              1
descriptor_volume_score_reference_mol2_filename              ../../003.gridbox/4zud.lig.min_scored.mol2
descriptor_volume_score_overlap_compute_method               analytical
descriptor_weight_fps_score                                  1
descriptor_weight_pharmacophore_score                        1
descriptor_weight_fingerprint_tanimoto                       -1
descriptor_weight_hms_score                                  1
descriptor_weight_volume_overlap_score                       -1
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
minimize_ligand                                              no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
chem_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/chem.defn
pharmacophore_defn_file                                      /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/ph4.defn
ligand_outfile_prefix                                        descriptor.output
write_footprints                                             yes
write_hbonds                                                 yes
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

Run the command using: 

dock6 -i rescore.in -o rescore.out

Several files should have been created. The descriptor.output_scored.mol2 file contains all of the molecules that would be deemed 'viable' in terms of mimicking the native crystal ligand interactions with the protein active site residues.

Footprint analysis plots can be generated for each molecule individually. Follow the steps provided in the previous tutorial: 2022 DOCK tutorial 2 with PDBID 4ZUD

Native crystal molecule for reference:

4ZUD minimized lig(1).png

The molecule with the smallest footprint score: 7.127408

4ZUD lowestFPscore denovo molecule new(1).png
Compoud221 footprint.txt.png

The molecule with the largest footprint score: 26.976864

4ZUD highestFPscore denovo molecule.png
Compoud193 footprint.txt.png
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